I-TASSER results

I-TASSER results for job id Rv1889c

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]

Input Sequence in FASTA format

>protein (118 residues)
MPRTNNDAWDLATSVGATATMVAAARAVATRADNPLIDDPFAEPLVRAVGIDFFTRWAAG
NIKATDVDDPDGTWGLQRLADLLAARTRYFDAFFRDATSAGIRQAVILASGLDARAYR

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MPRTNNDAWDLATSVGATATMVAAARAVATRADNPLIDDPFAEPLVRAVGIDFFTRWAAGNIKATDVDDPDGTWGLQRLADLLAARTRYFDAFFRDATSAGIRQAVILASGLDARAYR
Prediction	CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHCHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEHCCCCCCCCCC
Conf.Score	9887898765567766799999999999995999987895789988776668999987577654445676544566666765567888999999999998997899966786666789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MPRTNNDAWDLATSVGATATMVAAARAVATRADNPLIDDPFAEPLVRAVGIDFFTRWAAGNIKATDVDDPDGTWGLQRLADLLAARTRYFDAFFRDATSAGIRQAVILASGLDARAYR
Prediction	7644673413344332310120001001115475210404104300543236204412445254443645434442431341120212101410350175303000000023113447
	Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted Normalized B-facotr

(B-factor is a value to indicate the extent of the inherent thermal mobility of residues/atoms in proteins. In I-TASSER, this value is deduced from threading template proteins from the PDB in combination with the sequence profiles derived from sequence databases. The reported B-factor profile in the figure below corresponds to the normalized B-factor of the target protein, defined by B=(B'-u)/s, where B' is the raw B-factor value, u and s are respectively the mean and standard deviation of the raw B-factors along the sequence. (Click here to read more about predicted normalized B-factor)

Top 10 threading templates used by I-TASSER

Rank

PDB
Hit

Iden1

Iden2

Cov

Norm.
Zscore

Download
Align.

                  20                  40                  60                  80                 100

                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHCHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEHCCCCCCCCCC
MPRTNNDAWDLATSVGATATMVAAARAVATRADNPLIDDPFAEPLVRAVGIDFFTRWAAGNIKATDVDDPDGTWGLQRLADLLAARTRYFDAFFRDATSAGIRQAVILASGLDARAYR

2ckdA

0.45

0.42

0.93

1.03

MUSTER

--------WDIKTSVGTTAVMVAAARAAETDRPDALIRDPYAKLLVTNTGAGALWEAMLDPSMVAKVEDAEAAAMVEHMRSYQAVRTNFFDTYFNNAVIDGIRQFVILASGLDSRAYR

2ckdA

0.45

0.42

0.93

1.32

dPPAS

--------WDIKTSVGTTAVMVAAARAAETDRPDALIRDPYAKLLVTNTGAGALWEAMLDPSMVAKVEDAEAAAMVEHMRSYQAVRTNFFDTYFNNAVIDGIRQFVILASGLDSRAYR

2ckdA

0.44

0.41

0.93

2.23

wdPPAS

--------WDIKTSVGTTAVMVAAARAAETDRPDALIRDPYAKLLVTNTGAGALWEAMLDPVAKVEAIDAEAAAMVEHMRSYQAVRTNFFDTYFNNAVIDGIRQFVILASGLDSRAYR

2ckdA

0.44

0.41

0.92

1.28

wMUSTER

---------DIKTSVGTTAVMVAAARAAETDRPDALIRDPYAKLLVTNTGAGALWEAMLDPSMVAKVEDAEAAAMVEHMRSYQAVRTNFFDTYFNNAVIDGIRQFVILASGLDSRAYR

2ckdA

0.45

0.42

0.93

1.84

wPPAS

--------WDIKTSVGTTAVMVAAARAAETDRPDALIRDPYAKLLVTNTGAGALWEAMLDPSMVAKVEDAEAAAMVEHMRSYQAVRTNFFDTYFNNAVIDGIRQFVILASGLDSRAYR

2ckdA

0.45

0.42

0.93

4.22

dPPAS2

--------WDIKTSVGTTAVMVAAARAAETDRPDALIRDPYAKLLVTNTGAGALWEAMLDPSMVAKVEDAEAAAMVEHMRSYQAVRTNFFDTYFNNAVIDGIRQFVILASGLDSRAYR

2ckdA

0.45

0.42

0.93

1.46

PPAS

--------WDIKTSVGTTAVMVAAARAAETDRPDALIRDPYAKLLVTNTGAGALWEAMLDPSMVAKVEDAEAAAMVEHMRSYQAVRTNFFDTYFNNAVIDGIRQFVILASGLDSRAYR

2ckdA

0.44

0.41

0.93

1.68

Env-PPAS

--------WDIKTSVGTTAVMVAAARAAETDRPDALIRDPYAKLLVTNTGAGALWEAMLDPVAKVEAIDAEAAAMVEHMRSYQAVRTNFFDTYFNNAVIDGIRQFVILASGLDSRAYR

5cwiA2

0.13

0.12

0.93

0.81

MUSTER

-----ADIAKLCIKAASEAAEAASKAAELAQRHP---DSQAARDAIKLASQAAEAVKLACELAQEHPNADIAKKCIKAASEAAEEASKAAEEAQRQKARDEIKEASQKAEEVKERCER

5cwfA2

0.19

0.14

0.73

dPPAS

-------------SDEMAKVMLALAKAVLLAAKNN--DDEVAREIARAAAEIVEALRENNSDEMAKKMLELAKRVLDAAKNNDDETAREIARQAAEEVEAD-----------------

(a)	Iden1 is the number of template residues identical to query divided by number of aligned residues.
(b)	Iden2 is the number of template residues identical to query divided by query sequence length.
(c)	Cov is equal the number of aligned template residues divided by query sequence length.
(d)	Norm. Zscore is the normalized Z-score of the threading alignments. A Normalized Z-score >1 means a good alignment.
(e)	Download Align. list the threading program used to identify the template provide the 3D structure of aligned regions of threading templates.

Top 5 final models predicted by I-TASSER

(For each target, I-TASSER simulations generate a large ensemble of structural conformations, called decoys. To select the final models, I-TASSER uses the SPICKER program to cluster all the decoys based on the pair-wise structure similarity, and reports up to five models which corresponds to the five largest structure clusters. The confidence of each model is quantitatively measured by C-score that is calculated based on the significance of threading template alignments and the convergence parameters of the structure assembly simulations. C-score is typically in the range of [-5, 2], where a C-score of higher value signifies a model with a high confidence and vice-versa. TM-score and RMSD are estimated based on C-score and protein length following the correlation observed between these qualities. Since the top 5 models are ranked by the cluster size, it is possible that the lower-rank models have a higher C-score in rare cases. Although the first model has a better quality in most cases, it is also possible that the lower-rank models have a better quality than the higher-rank models as seen in our benchmark tests. If the I-TASSER simulations converge, it is possible to have less than 5 clusters generated. This is usually an indication that the models have a good quality because of the converged simulations.)

More about C-score

Local structure accuracy of first model

Download Model 1

C-score=-0.33

Estimated TM-score = 0.67±0.13

Estimated RMSD = 4.9±3.2Å

Download Model 2

C-score=-0.94

Download Model 3

C-score=-0.96

Download Model 4

C-score=-3.79

Download Model 5

C-score=-4.15

Proteins structureally close to the target in PDB (as identified by TM-align

(After the structure assembly simulation, I-TASSER uses the TM-align structural alignment program to match the first I-TASSER model to all structures in the PDB library. This section reports the top 10 proteins from the PDB that have the closest structural similarity, i.e. the highest TM-score, to the predicted I-TASSER model. Due to the structural similarity, these proteins often have similar function to the target. However, users are encouraged to use the data in the next section 'Predicted function using COACH' to infer the function of the target protein, since COACH has been extensively trained to derive biological functions from multi-source of sequence and structure features which has on average a higher accuracy than the function annotations derived only from the global structure comparison.)

Top 10 Identified stuctural analogs in PDB

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov
1	2ckdA	0.894	0.87	0.436	0.932
2	1rjeC	0.607	2.57	0.161	0.788
3	2zwaB1	0.551	3.59	0.039	0.848
4	3iwzD	0.538	4.07	0.028	0.822
5	5doqA	0.533	4.35	0.070	0.864
6	4zg8A	0.531	4.65	0.114	0.941
7	1ia7A	0.531	4.61	0.044	0.924
8	3kz4B	0.528	4.49	0.052	0.848
9	1t0rA1	0.523	3.86	0.082	0.788
10	3dhiA	0.513	3.93	0.081	0.780

(a)	Query structure is shown in cartoon, while the structural analog is displayed using backbone trace.
(b)	Ranking of proteins is based on TM-score of the structural alignment between the query structure and known structures in the PDB library.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov represents the coverage of the alignment by TM-align and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted function using COACH

(This section reports biological annotations of the target protein by COACH based on the I-TASSER structure prediction. COACH is a meta-server approach that combines multiple function annotation results from the COFACTOR, TM-SITE and S-SITE programs.)

Ligand binding sites

Rank	C-score	Cluster size	PDB Hit	Lig Name	Download Complex	Ligand Binding Site Residues
1	0.10	4	1xvgA	BRJ	Rep, Mult	19,22,23,26,83,87
2	0.08	3	4tt0B	IOD	Rep, Mult	85,86,89
3	0.08	3	3fu1A	ZN	Rep, Mult	87,91
4	0.05	2	1qghA	FE	Rep, Mult	91,95
5	0.05	2	1smyF	MG	Rep, Mult	26,83,86
6	0.05	2	1xvgA	BRJ	Rep, Mult	36,37,38,84,87,88
7	0.03	1	2uyqA	SAM	Rep, Mult	23,25,43,44,45,47
8	0.03	1	2uyqA	SAM	Rep, Mult	109,111
9	0.03	1	5sy7B	NUC	Rep, Mult	78,86

	Download the all possible binding ligands and detailed prediction summary.
	Download the templates clustering results.
(a)	C-score is the confidence score of the prediction. C-score ranges [0-1], where a higher score indicates a more reliable prediction.
(b)	Cluster size is the total number of templates in a cluster.
(c)	Lig Name is name of possible binding ligand. Click the name to view its information in the BioLiP database.
(d)	Rep is a single complex structure with the most representative ligand in the cluster, i.e., the one listed in the Lig Name column. Mult is the complex structures with all potential binding ligands in the cluster.

Enzyme Commission (EC) numbers and active sites

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov	EC Number	Active Site Residues
1	0.060	1qdbA	0.479	4.44	0.017	0.763	1.7.2.2	NA
2	0.060	1khoA	0.393	4.11	0.022	0.610	3.1.4.3	NA
3	0.060	1r5zA	0.484	5.02	0.104	0.924	3.6.3.14	94,96
4	0.060	1f8iA	0.491	4.25	0.044	0.797	4.1.3.1	86
5	0.060	2drsA	0.466	4.59	0.058	0.864	3.2.1.156	112
6	0.060	3gayA	0.460	4.21	0.019	0.746	4.1.2.13	NA
7	0.060	1clcA	0.490	4.57	0.106	0.873	3.2.1.4	NA
8	0.060	2yyjA	0.471	4.44	0.035	0.746	1.14.13.3	21
9	0.060	1og2A	0.439	4.61	0.043	0.771	1.14.14.1	NA
10	0.060	3bkkA	0.491	4.30	0.034	0.814	3.4.15.1	NA
11	0.060	1mhyD	0.498	4.19	0.100	0.797	1.14.13.25	87
12	0.060	1ei1A	0.468	4.83	0.052	0.856	5.99.1.3	NA
13	0.060	1fziA	0.512	3.91	0.062	0.771	1.14.13.25	87
14	0.060	1ia7A	0.531	4.61	0.044	0.924	3.2.1.4	NA
15	0.060	2jbmA	0.470	3.22	0.112	0.661	2.4.2.19	91
16	0.060	1ca1A	0.469	4.10	0.074	0.686	3.1.4.3	NA
17	0.060	3bnjA	0.447	4.35	0.044	0.729	1.7.2.2	NA
18	0.060	1rsrB	0.486	3.78	0.053	0.737	1.17.4.1	82
19	0.060	1j38A	0.473	4.42	0.093	0.746	3.4.15.1	NA

(a)	Cscore^EC is the confidence score for the EC number prediction. Cscore^EC values range in between [0-1]; where a higher score indicates a more reliable EC number prediction.
(b)	TM-score is a measure of global structural similarity between query and template protein.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

Gene Ontology (GO) terms

Rank	Cscore^GO	TM-score	RMSD^a	IDEN^a	Cov	PDB Hit	Associated GO Terms
Homologous GO templates in PDB
0	0.51	0.760	0.95	0.46	0.80	2uyoA	GO:0008168 GO:0016740 GO:0032259
1	0.21	0.894	0.87	0.44	0.93	2ckdA	GO:0008168 GO:0016740 GO:0032259
2	0.08	0.611	2.54	0.16	0.79	1rjdC	GO:0005829 GO:0006481 GO:0008168 GO:0010506 GO:0016740 GO:0018423 GO:0032259 GO:0043623
3	0.07	0.496	3.41	0.08	0.72	1rjgA	GO:0005829 GO:0006481 GO:0008168 GO:0010506 GO:0016740 GO:0018423 GO:0032259 GO:0043623
4	0.07	0.590	2.15	0.17	0.70	3p71T	GO:0003880 GO:0005829 GO:0006464 GO:0006479 GO:0006481 GO:0008168 GO:0008276 GO:0008757 GO:0010906 GO:0016740 GO:0018423 GO:0031333 GO:0032259 GO:0042981 GO:0090266
5	0.07	0.448	3.26	0.18	0.66	3o7wA	GO:0003880 GO:0005829 GO:0006464 GO:0006479 GO:0006481 GO:0008168 GO:0008276 GO:0008757 GO:0010906 GO:0016740 GO:0018423 GO:0031333 GO:0032259 GO:0042981 GO:0090266
6	0.07	0.551	3.59	0.04	0.85	2zwaB	GO:0005737 GO:0005739 GO:0005829 GO:0006400 GO:0008033 GO:0008168 GO:0008175 GO:0008757 GO:0016740 GO:0030488 GO:0031591 GO:0032259
7	0.06	0.394	5.04	0.05	0.72	3tiiB	GO:0000166 GO:0006464 GO:0046872
8	0.06	0.309	5.14	0.06	0.61	3fdsA	GO:0000287 GO:0003677 GO:0003684 GO:0003887 GO:0005737 GO:0006260 GO:0006261 GO:0006281 GO:0006974 GO:0016740 GO:0016779 GO:0046872 GO:0071897
9	0.06	0.322	4.75	0.06	0.60	4k2dA	GO:0015035 GO:0042597 GO:0045454 GO:0055114
10	0.06	0.327	4.95	0.06	0.59	4mkiA	GO:0000166 GO:0005524 GO:0005886 GO:0006810 GO:0016020 GO:0016787 GO:0016887 GO:0043190
11	0.06	0.321	5.20	0.03	0.65	4f4wA	GO:0000287 GO:0003677 GO:0003684 GO:0003887 GO:0005737 GO:0006260 GO:0006261 GO:0006281 GO:0006974 GO:0016740 GO:0016779 GO:0046872 GO:0071897
12	0.06	0.326	4.70	0.02	0.61	4dcmA	GO:0003676 GO:0005737 GO:0006364 GO:0008168 GO:0008990 GO:0016740 GO:0031167 GO:0032259 GO:0052916 GO:0070475
13	0.06	0.368	4.34	0.11	0.63	3ggdA
14	0.06	0.318	5.39	0.04	0.66	3jwhA	GO:0001510 GO:0008171 GO:0008173
15	0.06	0.333	4.68	0.00	0.57	3lyhB	GO:0009236 GO:0016852
16	0.06	0.324	4.00	0.04	0.50	1q6aA	GO:0006468 GO:0007623 GO:0042802 GO:0048511
17	0.06	0.263	5.29	0.04	0.53	3kvtA	GO:0005216 GO:0005244 GO:0005249 GO:0005267 GO:0006810 GO:0006811 GO:0006813 GO:0008076 GO:0016020 GO:0016021 GO:0034765 GO:0046872 GO:0051260 GO:0055085 GO:0071805
18	0.06	0.267	4.89	0.04	0.49	3ougA	GO:0004068 GO:0005737 GO:0006523 GO:0015940 GO:0016829 GO:0016831

Consensus prediction of GO terms

Molecular Function	GO:0003880	GO:0008757
GO-Score	0.39	0.39
Biological Processes	GO:0018410	GO:0006479
GO-Score	0.39	0.39
Cellular Component	GO:0044444
GO-Score	0.39

(a)	Cscore^GO is a combined measure for evaluating global and local similarity between query and template protein. It's range is [0-1] and higher values indicate more confident predictions.
(b)	TM-score is a measure of global structural similarity between query and template protein.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.
(f)	The second table shows a consensus GO terms amongst the top scoring templates. The GO-Score associated with each prediction is defined as the average weight of the GO term, where the weights are assigned based on Cscore^GO of the template.

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]

Please cite the following articles when you use the I-TASSER server:
1.	J Yang, R Yan, A Roy, D Xu, J Poisson, Y Zhang. The I-TASSER Suite: Protein structure and function prediction. Nature Methods, 12: 7-8, 2015.
2.	J Yang, Y Zhang. I-TASSER server: new development for protein structure and function predictions, Nucleic Acids Research, 43: W174-W181, 2015.
3.	A Roy, A Kucukural, Y Zhang. I-TASSER: a unified platform for automated protein structure and function prediction. Nature Protocols, 5: 725-738, 2010.
4.	Y Zhang. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9: 40, 2008.